fix problems in unittests after putting into separated folders

config.py

@@ -0,0 +1,28 @@
+import os
+
+
+class Config:
+    """
+        This class defines some general configs
+
+        Attributes
+        ----------
+        TEST_MIXTURE_METADATA_EXTRACTION_EXPECTED_VALUE: str
+            get the expected value to compare with the actual one
+        """
+
+    TEST_MIXTURE_METADATA_EXTRACTION_EXPECTED_VALUE = "{'operator_date': '2014-06-30', 'tester_name': 'Werner', 'specimen_name': 'BA-Losert MI', 'cement--QuantityInMix': 330.0, 'cement--BulkDensity': 3.123, 'cement--Volume': 105.7, 'cement--Annotation': 'CEM I 42.5 R', 'water_total--QuantityInMix': 175.0, 'water_total--BulkDensity': 1.0, 'water_total--Volume': 175.0, 'water_cement_ratio': 0.5303030303030303, 'water_effective--QuantityInMix': nan, 'water_effective--BulkDensity': nan, 'water_effective--Volume': nan, 'air_content--QuantityInMix': 0.0, 'air_content--BulkDensity': 0.0, 'air_content--Volume': 20.0, 'addition1--QuantityInMix': 273.0, 'addition1--BulkDensity': 2.74, 'addition1--Volume': 99.6, 'addition1--Annotation': 'Medenbach - Kalksteinmehl', 'admixture--QuantityInMix': 5.61, 'admixture--BulkDensity': 1.05, 'admixture--Volume': 5.3, 'admixture--Annotation': 'FM 595 BASF', 'aggregate--QuantityInMix': 1564.0, 'aggregate--BulkDensity': nan, 'aggregate--Volume': 594.4000000000001}"
+
+    TEST_METADATA_EXTRACTION_EXPECTED_VALUE = {'experimentName': 'BA-Losert MI E-Modul 28d v. 04.08.14 Probe 4',
+                                               'software_specification': 'MTS793|MPT|DEU|1|2|,|.|:|49|1|1|A',
+                                               'operator_timestamp': '13:25:39',
+                                               'operator_date': '01.09.2014',
+                                               'tester_name': 'Kh',
+                                               'specimen_name': 'BA-Losert E-Modul 28d v. 04.08.14 Probe 4',
+                                               'remark': 'Kraftgeregelt 3,9 kN/s',
+                                               'weight': 5342.0,
+                                               'weight_unit': 'g',
+                                               'diameter': 98.6,
+                                               'length': 300.3,
+                                               'length_unit': 'mm',
+                                               'mix_file': '2014_08_05 Rezeptur_MI.xlsx'}

tests/data_extraction/test_mapping_script.py

@@ -1,117 +1,121 @@
-import pytest
+import unittest
 import rdflib
 import datetime
 import os
 import yaml
-
 from pathlib import Path
 
 from lebedigital.mapping.emodul_mapping import generate_knowledge_graph, get_date_time_value
 
-def query_and_test_result(typeOfQuery, predicate, prop, g):
-    print(f"""Query for {typeOfQuery}:""")
-    q = f"""
-            SELECT ?o WHERE {{
-                    {predicate} {prop} ?o .
-            }}
-            """
-    print(q)
-    result = g.query(q)
-    return result
-
-def print_next():
-    print("Pass")
-    print("###################Next Query#####################################")
-
-def print_first():
-    print("###################First Query####################################")
-
-def test_generate_knowledge_graph():
-    metadataPath = 'testMetaData.yaml'
-    filename = "knowledgeGraph.ttl"
-    print("Start testing:")
-    #Generate a testMetadata file
-    print("Generate metadata file for test:")
-    target_data = {'experimentName': 'BA-Losert MI E-Modul 28d v. 04.08.14 Probe 4',
-            'software_specification': 'MTS793|MPT|DEU|1|2|,|.|:|49|1|1|A',
-            'operator_timestamp': '13:25:39',
-            'operator_date': '01.09.2014',
-            'tester_name': 'Kh',
-            'specimen_name': 'BA-Losert E-Modul 28d v. 04.08.14 Probe 4',
-            'remark': 'Kraftgeregelt 3,9 kN/s',
-            'weight': 5342.0,
-            'weight_unit': 'g',
-            'diameter': 98.6,
-            'length': 300.3,
-            'length_unit': 'mm',
-            'mix_file': '2014_08_05 Rezeptur_MI.xlsx'}
-
-    with open(metadataPath, 'w') as yamlFile:
-        yaml.dump(target_data, yamlFile)
-    print("Generate knowledgeGraph:")
-    generate_knowledge_graph(metadataPath, filename)
-
-    g = rdflib.Graph()
-    result = g.parse(filename, format='ttl')
-    print("Query knowledgeGraph:")
-
-    print_first()
-
-    result = query_and_test_result('diameter','ns1:informationbearingentity1', 
-                        'ns7:has_decimal_value', g)
-    for row in result:
-        assert target_data['diameter'] == float(row.o)
-
-    print_next()
-
-    result = query_and_test_result('length', 'ns1:informationbearingentity2',
-                        'ns7:has_decimal_value', g)
-    for row in result:
-        assert target_data['length'] == float(row.o)
-
-    print_next()
-
-    result = query_and_test_result('weight', 'ns1:informationbearingentity3',
-                        'ns7:has_decimal_value', g)
-    for row in result:
-        assert target_data['weight'] == float(row.o)
-
-    print_next()
-
-    time = get_date_time_value(target_data)
-    result = query_and_test_result('operator_time', 'ns1:informationbearingentity6',
-                        'ns1:has_datetime_value', g)
-    for row in result:
-       assert time == datetime.datetime.strptime(str(row.o).replace('T',' '), "%Y-%m-%d %H:%M:%S")
-
-    print_next()
-
-    result = query_and_test_result('operatorName', 'ns1:informationbearingentity7', 
-            'ns7:has_text_value', g)
-    for row in result:
-        assert target_data['tester_name'] == str(row.o)
-
-    print_next()
-    result = query_and_test_result('rawFileName', 'ns1:informationbearingentity4', 
-            'ns7:has_text_value', g)
-    for row in result:
-        assert target_data['experimentName'] == str(row.o)
-
-    print_next()
-    result = query_and_test_result('rawFileName', 'ns1:informationbearingentity5', 
-            'ns7:has_text_value', g)
-    rawPath = os.path.join(Path(__file__).parents[2], 'usecases', 
-            'MinimumWorkingExample', 'Data', 'E-modul', target_data['experimentName'])
-
-    for row in result:
-        assert rawPath == str(row.o)
-
-    print('Pass all tests')
-
-    print("Deleting test files:")
-    os.remove(filename)
-    os.remove(metadataPath)
-
-    print("End testing")
-
-#test_generate_knowledge_graph()
+class TestMappingScript(unittest.TestCase):
+
+    def query_and_test_result(self, typeOfQuery, predicate, prop, g):
+        print(f"""Query for {typeOfQuery}:""")
+        q = f"""
+                SELECT ?o WHERE {{
+                        {predicate} {prop} ?o .
+                }}
+                """
+        print(q)
+        result = g.query(q)
+        return result
+
+
+    def print_next(self):
+        print("Pass")
+        print("###################Next Query#####################################")
+
+
+    def print_first(self):
+        print("###################First Query####################################")
+
+
+    def test_generate_knowledge_graph(self):
+        metadataPath = 'testMetaData.yaml'
+        filename = "knowledgeGraph.ttl"
+        print("Start testing:")
+        # Generate a testMetadata file
+        print("Generate metadata file for test:")
+        target_data = {'experimentName': 'BA-Losert MI E-Modul 28d v. 04.08.14 Probe 4',
+                       'software_specification': 'MTS793|MPT|DEU|1|2|,|.|:|49|1|1|A',
+                       'operator_timestamp': '13:25:39',
+                       'operator_date': '01.09.2014',
+                       'tester_name': 'Kh',
+                       'specimen_name': 'BA-Losert E-Modul 28d v. 04.08.14 Probe 4',
+                       'remark': 'Kraftgeregelt 3,9 kN/s',
+                       'weight': 5342.0,
+                       'weight_unit': 'g',
+                       'diameter': 98.6,
+                       'length': 300.3,
+                       'length_unit': 'mm',
+                       'mix_file': '2014_08_05 Rezeptur_MI.xlsx'}
+
+        with open(metadataPath, 'w') as yamlFile:
+            yaml.dump(target_data, yamlFile)
+        print("Generate knowledgeGraph:")
+        generate_knowledge_graph(metadataPath, filename)
+
+        g = rdflib.Graph()
+        result = g.parse(filename, format='ttl')
+        print("Query knowledgeGraph:")
+
+        self.print_first()
+
+        result = self.query_and_test_result('diameter', 'ns1:informationbearingentity1',
+                                       'ns7:has_decimal_value', g)
+        for row in result:
+            self.assertEqual(target_data['diameter'], float(row.o))
+
+        self.print_next()
+
+        result = self.query_and_test_result('length', 'ns1:informationbearingentity2',
+                                       'ns7:has_decimal_value', g)
+        for row in result:
+            self.assertEqual(target_data['length'], float(row.o))
+
+        self.print_next()
+
+        result = self.query_and_test_result('weight', 'ns1:informationbearingentity3',
+                                       'ns7:has_decimal_value', g)
+        for row in result:
+            self.assertEqual(target_data['weight'], float(row.o))
+
+        self.print_next()
+
+        time = get_date_time_value(target_data)
+        result = self.query_and_test_result('operator_time', 'ns1:informationbearingentity6',
+                                       'ns1:has_datetime_value', g)
+        for row in result:
+            self.assertEqual(time, datetime.datetime.strptime(str(row.o).replace('T', ' '), "%Y-%m-%d %H:%M:%S"))
+
+        self.print_next()
+
+        result = self.query_and_test_result('operatorName', 'ns1:informationbearingentity7',
+                                       'ns7:has_text_value', g)
+        for row in result:
+            self.assertEqual(target_data['tester_name'], str(row.o))
+
+        self.print_next()
+        result = self.query_and_test_result('rawFileName', 'ns1:informationbearingentity4',
+                                       'ns7:has_text_value', g)
+        for row in result:
+            self.assertEqual(target_data['experimentName'], str(row.o))
+
+        self.print_next()
+        result = self.query_and_test_result('rawFileName', 'ns1:informationbearingentity5',
+                                       'ns7:has_text_value', g)
+        rawPath = os.path.join(Path(__file__).parents[2], 'usecases',
+                               'MinimumWorkingExample', 'Data', 'E-modul', target_data['experimentName'])
+
+        for row in result:
+            self.assertEqual(rawPath, str(row.o))
+
+        print('Pass all tests')
+
+        print("Deleting test files:")
+        os.remove(filename)
+        os.remove(metadataPath)
+
+        print("End testing")
+
+    # test_generate_knowledge_graph()

tests/data_extraction/test_metadata_extraction_emodul.py

@@ -1,32 +1,21 @@
-import pytest
+import unittest
+from config import Config
 
 from lebedigital.raw_data_processing.youngs_modulus_data \
     .emodul_metadata_extraction import extract_metadata_emodulus
+class TestMetaDataExtractionEmodul(unittest.TestCase):
+    def test_metadata_extraction_emodul(self):
+        """Tesing the metadata extraction on a single example"""
 
-def test_metadata_extraction_emodul():
-    """Tesing the metadata extraction on a single example"""
+        # setting up the test example
+        input = '../usecases/MinimumWorkingExample/Data/E-modul/BA-Losert MI E-Modul 28d v. 04.08.14 Probe 4'
+        mix_file = 'mix.dat'
+        specimen_file = 'specimen.dat'
 
-    # setting up the test example
-    input = '../usecases/MinimumWorkingExample/Data/E-modul/BA-Losert MI E-Modul 28d v. 04.08.14 Probe 4'
-    mix_file = 'mix.dat'
-    specimen_file = 'specimen.dat'
+        target_data = Config.TEST_METADATA_EXTRACTION_EXPECTED_VALUE
 
-    target_data = {'experimentName': 'BA-Losert MI E-Modul 28d v. 04.08.14 Probe 4',
-                   'software_specification': 'MTS793|MPT|DEU|1|2|,|.|:|49|1|1|A',
-                   'operator_timestamp': '13:25:39',
-                   'operator_date': '01.09.2014',
-                   'tester_name': 'Kh',
-                   'specimen_name': 'BA-Losert E-Modul 28d v. 04.08.14 Probe 4',
-                   'remark': 'Kraftgeregelt 3,9 kN/s',
-                   'weight': 5342.0,
-                   'weight_unit': 'g',
-                   'diameter': 98.6,
-                   'length': 300.3,
-                   'length_unit': 'mm',
-                   'mix_file': '2014_08_05 Rezeptur_MI.xlsx'}
+        # run extraction and getting a dictionary with metadata
+        test_data = extract_metadata_emodulus(input, specimen_file, mix_file)
 
-    # run extraction and getting a dictionary with metadata
-    test_data = extract_metadata_emodulus(input, specimen_file, mix_file)
-
-    # checking if result is correct
-    assert test_data == target_data
+        # checking if result is correct
+        self.assertEqual(test_data, target_data)

tests/data_extraction/test_mixture_metadata_extraction.py

@@ -1,55 +1,27 @@
-import pytest
-from lebedigital.raw_data_processing.metadata_extraction \
-    .mixture_metadata_extraction import extraction
-
-
-def test_extraction():
-    """Tesing the mixture metadata extraction on a single example"""
-
-    # setting up the test example
-    input = '../usecases/MinimumWorkingExample/Data/Mischungen/2014_08_05 Rezeptur_MIII.xlsx'
-    target_data = {'Cement -- Quantity in mix': 330, 'Cement -- Specific gravity': 3.123,
-                   'Cement -- Annotation': 'CEM I 42,5 R', 'Water (total) -- Quantity in mix':
-                    175, 'Water (total) -- Specific gravity': 1, 'Water (total) -- Annotation': 
-                    '---', 'Water (effective) -- Quantity in mix': 
-                    '---', 'Water (effective) -- Specific gravity': 
-                    '---', 'Water (effective) -- Annotation': '---', 'Air -- Quantity in mix': 
-                    '---', 'Air -- Specific gravity': '---', 'Air -- Annotation': '---', 
-                    'Supplementary cementious materials Kalksteinmehl -- Quantity in mix': 147, 
-                    'Supplementary cementious materials Kalksteinmehl -- Specific gravity': 2.74,
-                    'Supplementary cementious materials Kalksteinmehl -- Annotation': 
-                    'Medenbach', 'Admixture -- Quantity in mix': 4.95, 
-                    'Admixture -- Specific gravity': 1.05, 'Admixture -- Annotation': 
-                    'FM 595 BASF', 'Total -- Quantity in mix': 656.95, 
-                    'Total -- Specific gravity': '---', 'Total -- Annotation': '---', 
-                    'Zuschlag (total) -- Quantity in mix': 1685, 
-                    'Zuschlag (total) -- Specific gravity': '---', 
-                    'Zuschlag (total) -- Annotation': '---', '0 / 0,3 -- Quantity in mix': 0, 
-                    '0 / 0,3 -- Specific gravity': 2.65, '0 / 0,3 -- Annotation': 'Quarz', 
-                    '0,1 / 0,5 -- Quantity in mix': 337, '0,1 / 0,5 -- Specific gravity': 2.63, 
-                    '0,1 / 0,5 -- Annotation': 'Okrilla  ', '0,5 / 1,0 -- Quantity in mix': 194, 
-                    '0,5 / 1,0 -- Specific gravity': 2.63,
-                    '0,5 / 1,0 -- Annotation': 'Okrilla  ', '1,0 / 2,0 -- Quantity in mix': 194, 
-                    '1,0 / 2,0 -- Specific gravity': 2.63, '1,0 / 2,0 -- Annotation': 'Okrilla  ', 
-                    '2,0 / 4,0 -- Quantity in mix': 126, '2,0 / 4,0 -- Specific gravity': 2.63, 
-                    '2,0 / 4,0 -- Annotation': 'Okrilla  ', '4,0 / 8,0 -- Quantity in mix': 126, 
-                    '4,0 / 8,0 -- Specific gravity': 2.63, '4,0 / 8,0 -- Annotation': 'Okrilla  ', 
-                    '8,0 / 16,0 -- Quantity in mix': 708, '8,0 / 16,0 -- Specific gravity': 2.63, 
-                    '8,0 / 16,0 -- Annotation': 'Okrilla  ', 'nan -- Quantity in mix': '---', 
-                    'nan -- Specific gravity': '---', 'nan -- Annotation': '---', 
-                    'Fresh concrete -- Quantity in mix': 2341.95, 
-                    'Fresh concrete -- Specific gravity': '---', 'Fresh concrete -- Annotation': 
-                    '---', 'Mehlkornanteil -- Quantity in mix': '---', 
-                    'Mehlkornanteil -- Specific gravity': '---', 'Mehlkornanteil -- Annotation': 
-                    '---', 'Mörtelanteil -- Quantity in mix': '---', 
-                    'Mörtelanteil -- Specific gravity': '---', 'Mörtelanteil -- Annotation': '---', 
-                    'Date': '2014-06-30', 'Editor': 'Werner', 'Requester': 'BAM 7.0', 
-                    'Project number': 'BA-Losert', 'Specimen': 'BA-Losert MIII', 
-                    'Betonsorte u -festigkeitsklasse': '---', 'Wasserzementwert': '0,53 w/b = 0,37', 
-                    'Konsistenz': 'SVB', 'Sieblinie n. DIN 1045': 'SVB', 'Körnungsziffer': 3.88, 
-                    'Vol Leim/Zuschlag': 56.00624024960999}
-    # run extraction and getting a dictionary with metadata
-    test_data = extraction(input, None)
-
-    # checking if result is correct
-    assert test_data == target_data
+import os
+from lebedigital.raw_data_processing.mixture \
+    .mixture_metadata_extraction import extract_metadata_mixture
+from config import Config
+import unittest
+
+
+class TestMixtureMetadataExtraction(unittest.TestCase):
+    def test_extraction(self):
+        """Testing the mixture metadata extraction on a single example"""
+
+        # setting up the test example input
+        input_path = '../usecases/MinimumWorkingExample/Data/Mischungen/2014_08_05 Rezeptur_MI.xlsx'
+
+        target_data = Config.TEST_MIXTURE_METADATA_EXTRACTION_EXPECTED_VALUE
+        # run extraction and getting a dictionary with metadata
+        test_data = extract_metadata_mixture(input_path, None)
+
+        # make sure if the path exists
+        self.assertTrue(os.path.exists(input_path))
+
+        # checking if result is correct
+        self.assertEqual(test_data.__str__(), target_data)
+
+
+if __name__ == '__main__':
+    unittest.main()